addAnnotation with seqRef

[jalview.git] / src / jalview / datamodel / AlignmentI.java

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 10ea154..ebfb0ce 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -225,11 +225,6 @@ public interface AlignmentI
      */\r
     public void addAnnotation(AlignmentAnnotation aa);\r
 \r
-    /**\r
-     * Adds a new AlignmentAnnotation to this alignment,\r
-     *  associated to Sequence starting at sequence index\r
-     */\r
-    public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef);\r
 \r
     public void setAnnotationIndex(AlignmentAnnotation aa, int index);\r
 \r
@@ -292,7 +287,8 @@ public interface AlignmentI
      */\r
     public boolean padGaps();\r
 \r
-     public void adjustSequenceAnnotations();\r
+    public void adjustSequenceAnnotations();\r
 \r
+    public HiddenSequences getHiddenSequences();\r
 \r
 }\r